Experimental study of the effect of disorder on DNA dynamics in post arrays during electrophoresis.

We used top-down fabrication techniques to create both an ordered hexagonal array and a disordered array of 1 μm diameter cylindrical posts in a silicon dioxide microchannel with the same number of posts per unit area. The electrophoretic mobility and dispersion coefficient of λ DNA in each of the arrays were obtained as a function of the electric field using ensembles of DNA molecules in a double channel device that minimizes experimental artifacts. To deepen our understanding of the transport, we also used fluorescence microscopy to examine the dynamics of single DNA molecules as they interact with the arrays at a fixed value of the electric field. Based on the results of these two types of experiments, we conclude that the electrophoretic mobility is not dependent on the array order but that band broadening in the device is greater in the disordered array.